MHC genotyping from rhesus macaque exome sequences

[1]  Yukinori Okada,et al.  Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data , 2019, Scientific Reports.

[2]  J. Hoxie,et al.  Polymorphisms in Rhesus Macaque Tetherin Are Associated with Differences in Acute Viremia in Simian Immunodeficiency Virus Δnef-Infected Animals , 2018, Journal of Virology.

[3]  T. Marquès-Bonet,et al.  Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model , 2018, Scientific Reports.

[4]  Sven Rahmann,et al.  Genome analysis , 2022 .

[5]  K. Chatfield,et al.  The use of non-human primates in research and testing , 2002, Animal Welfare.

[6]  D. O’Connor,et al.  Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques , 2017, Immunogenetics.

[7]  Brian Bushnell,et al.  BBMerge – Accurate paired shotgun read merging via overlap , 2017, PloS one.

[8]  D. O’Connor,et al.  Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques , 2017, bioRxiv.

[9]  D. Watkins,et al.  The role of MHC class I gene products in SIV infection of macaques , 2017, Immunogenetics.

[10]  R. Ramakrishnan,et al.  Whole genome sequencing predicts novel human disease models in rhesus macaques. , 2017, Genomics.

[11]  E. Kirkness,et al.  Fast and accurate HLA typing from short-read next-generation sequence data with xHLA , 2017, Proceedings of the National Academy of Sciences.

[12]  Jerzy K. Kulski,et al.  Comparative genomics of the human, macaque and mouse major histocompatibility complex , 2017, Immunology.

[13]  Alexander Schönhuth,et al.  De novo assembly of viral quasispecies using overlap graphs , 2017, bioRxiv.

[14]  James Robinson,et al.  IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex , 2016, Nucleic Acids Res..

[15]  D. O’Connor,et al.  The orthologs of HLA-DQ and -DP genes display abundant levels of variability in macaque species , 2016, Immunogenetics.

[16]  Trent M. Prall,et al.  Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques , 2016, bioRxiv.

[17]  D. O’Connor,et al.  Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities , 2016, Immunogenetics.

[18]  R. Gibbs,et al.  The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences , 2016, Genome research.

[19]  R. Norgren,et al.  Exome screening to identify loss-of-function mutations in the rhesus macaque for development of preclinical models of human disease , 2016, BMC Genomics.

[20]  Chad A Shaw,et al.  Molecular Diagnostic Experience of Whole-Exome Sequencing in Adult Patients , 2015, Genetics in Medicine.

[21]  T. Karlsen,et al.  Development of a high-resolution NGS-based HLA-typing and analysis pipeline , 2015, Nucleic acids research.

[22]  Ankita Patel,et al.  Molecular findings among patients referred for clinical whole-exome sequencing: Editorial comment , 2015 .

[23]  Magalie S Leduc,et al.  Molecular findings among patients referred for clinical whole-exome sequencing. , 2014, JAMA.

[24]  Melisa L. Budde,et al.  Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication , 2014, Genome Biology.

[25]  J. Rogers,et al.  Genome typing of nonhuman primate models: implications for biomedical research. , 2014, Trends in genetics : TIG.

[26]  EricsenAdam,et al.  Candidate Loci Associated with AIDS Virus Replication Identified by Whole Genome Sequencing of SIV-Infected Macaques , 2014 .

[27]  Guillaume Marçais,et al.  A new rhesus macaque assembly and annotation for next-generation sequencing analyses , 2014, Biology Direct.

[28]  D. O’Connor,et al.  Survey of major histocompatibility complex class II diversity in pig-tailed macaques , 2014, Immunogenetics.

[29]  Magalie S Leduc,et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. , 2013, The New England journal of medicine.

[30]  V. Simon,et al.  APOBEC3G Polymorphism as a Selective Barrier to Cross-Species Transmission and Emergence of Pathogenic SIV and AIDS in a Primate Host , 2013, PLoS pathogens.

[31]  Xun Xu,et al.  An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing , 2013, PloS one.

[32]  S. Lank,et al.  Major Histocompatibility Complex Class I Haplotype Diversity in Chinese Rhesus Macaques , 2013, G3: Genes, Genomes, Genetics.

[33]  Rui Chen,et al.  Exome Sequencing by Targeted Enrichment , 2013, Current protocols in molecular biology.

[34]  R. Norman,et al.  Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform , 2013, Microbiome.

[35]  D. O’Connor,et al.  Haplessly hoping: macaque major histocompatibility complex made easy. , 2013, ILAR journal.

[36]  Sven Rahmann,et al.  Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.

[37]  A. Kimura,et al.  Association of Major Histocompatibility Complex Class I Haplotypes with Disease Progression after Simian Immunodeficiency Virus Challenge in Burmese Rhesus Macaques , 2012, Journal of Virology.

[38]  E. Vallender Expanding whole exome resequencing into non-human primates , 2011, Genome Biology.

[39]  P. Yu,et al.  Association of major histocompatibility complex class I chain-related gene A microsatellite polymorphism and hepatocellular carcinoma in South China Han population. , 2011, Tissue antigens.

[40]  D. Watkins,et al.  The TRIM5α Genotype of Rhesus Macaques Affects Acquisition of Simian Immunodeficiency Virus SIVsmE660 Infection after Repeated Limiting-Dose Intrarectal Challenge , 2011, Journal of Virology.

[41]  James Robinson,et al.  IPD—the Immuno Polymorphism Database , 2012, Nucleic Acids Res..

[42]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[43]  James Robinson,et al.  IPD—the Immuno Polymorphism Database , 2004, Nucleic acids research.

[44]  T. Harkins,et al.  Major histocompatibility complex genotyping with massively parallel pyrosequencing , 2009, Nature Medicine.

[45]  John Sidney,et al.  Two MHC Class I Molecules Associated with Elite Control of Immunodeficiency Virus Replication, Mamu-B*08 and HLA-B*2705, Bind Peptides with Sequence Similarity12 , 2009, The Journal of Immunology.

[46]  James G. R. Gilbert,et al.  Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project , 2008, Immunogenetics.

[47]  D. Watkins,et al.  Molecular typing of major histocompatibility complex class I alleles in the Indian rhesus macaque which restrict SIV CD8+ T cell epitopes , 2007, Immunogenetics.

[48]  M. Carrington,et al.  Mamu-B*08-Positive Macaques Control Simian Immunodeficiency Virus Replication , 2007, Journal of Virology.

[49]  Bernhard Moser,et al.  On the T , 2006, Fuzzy Sets Syst..

[50]  K. Christopher Garcia,et al.  How the T Cell Receptor Sees Antigen—A Structural View , 2005, Cell.

[51]  Gustavo Glusman,et al.  Genetic divergence of the rhesus macaque major histocompatibility complex. , 2004, Genome research.

[52]  Todd M. Allen,et al.  Expression of the Major Histocompatibility Complex Class I Molecule Mamu-A*01 Is Associated with Control of Simian Immunodeficiency Virus SIVmac239 Replication , 2003, Journal of Virology.

[53]  M. Krawczak,et al.  MHC Class I Alleles Influence Set-Point Viral Load and Survival Time in Simian Immunodeficiency Virus-Infected Rhesus Monkeys1 , 2002, The Journal of Immunology.

[54]  T. Williams Human leukocyte antigen gene polymorphism and the histocompatibility laboratory. , 2001, The Journal of molecular diagnostics : JMD.

[55]  U. Göbel,et al.  Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. , 1997, FEMS microbiology reviews.

[56]  D. Wiley,et al.  Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1 , 1993, Nature.

[57]  P. Parham,et al.  Rapid cloning of HLA-A,B cDNA by using the polymerase chain reaction: frequency and nature of errors produced in amplification. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[58]  B. Malissen,et al.  Exon/intron organization and complete nucleotide sequence of an HLA gene. , 1982, Proceedings of the National Academy of Sciences of the United States of America.